On July 1st I will start a post-doc in Wageningen, The Netherlands at the WUR. More precisely, with a post-doc in the group of Prof. Van Eeuwijk at Biometris, cooperating with the group of Prof. Hall at Plant Research International (PRI), within the framework of the new Netherlands Metabolomics Center.

Lately, Chemical blogspace has seen an interesting discussion on the quality of opendata and free chemical database (over 32 free resources now ), such as the NMRShiftDB.org. For example, see Antony’s view on the NMRShiftDB and Robien’s analysis.

Only few people are using InChI’s to indicate the molecules the blog about (prominent exceptions are Useful Chemistry and Molecule of the Day). Consequently, the number of detected molecules (without using OSCAR3) in Chemical blogspace has been low.

Last year the Programmeerzomer.nl sponsored one summer student to work on Bioclipse (see the announcement ). The Programmeerzomer is much like the Google Summer of Code where I mentor Alexandr. However, it is much smaller and oriented at just the NL area: both the student and the mentor needs to be Dutch, but the opensource project does not.

While looking up a reference for FirstGlance in Jmol, I found Janocchio, a CDK and Jmol based tool for prediction of coupling constants, recently published in Magnetic Resonance in Chemistry. It’s written by Evans, Bodkin, Baker and Sharman (from Eli Lilly) and licensed LGPL. It is one of those rare contributions of pharmaceutical industry, and I can only deeply appreciate this contribution.

Some 7 years ago, following successes in physics, ChemWeb.com launched the Chemistry Preprint Server (CPS), and Warr evaluated it in a JCIM article three years later. She wrote about ‘lessons learned’, but the only one seemed to have been that chemistry was not ready for it, as the project shutdown in 2004. The archives are still available, fortunately, and you may find it amusing to look up my or some other submission.

Dealing with scientific literature has been one important theme in Chemical blogspace. For example, ranking articles and how to store your personal PDF archive has been topics of discussion. In this blog I will summarize bits of the discussion, and my personal view on things.

I just finished setting up a Blue Obelisk section for Chemical blogspace, as future replacement for the current Planet Blue Obelisk (unless someone wants to take over that webpage). The only thing really missing is a RSS feed for recent posts for just the Blue Obelisk member blogs (BTW, just email me if you want to be listed as BO member with your blog too; the BO community is very open!).

Now that my CUBIC desktop machine is shutting down, I made the necessary backups, among a mail.tar for my mail correspondence of about a year. About 500MB in size for almost 8700 files. Strigi is a perfect tool to help me find messages in this archive, as it will recurse into the .tar archive, and even into email attachements.

Mitch just launched ChemRank, a website where we can comment on and vote thumbs up or down for scientific articles. Good initiative I think.

Some time ago I wrote a small Perl script to convert a decision tree created with Weka in the ARFF format to Java source code, for use in the ionization potential prediction in CDK. The advantage is that Weka is no longer used are runtime, and that there is no model that needs to be loaded and interpreted. Instead, it is simple Java code that does the work, much faster.